BN0662 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.2780e-08 4.1666e-05
Layer 4 8.3148e-08 1.5731e-05
Layer 5 1.1478e-05 6.7026e-04
Layer 6 9.3392e-05 2.7991e-03
Layer 2 9.0359e-04 4.8733e-02
WM 3.1888e-01 3.7780e-01
Layer 1 9.3170e-01 6.9532e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
INPP5F Expression Distribution
Gene Specificity Score (GSS)
INPP5F GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
INPP5F Layer 4 2.6660 0.7818
NUAK1 Layer 4 3.0645 0.7747
RIMS3 Layer 4 3.1523 0.7730
KCNC2 Layer 4 3.0117 0.7729
NAP1L5 Layer 4 2.9277 0.7681
CPLX1 Layer 4 2.7422 0.7639
ACSL6 Layer 4 2.8398 0.7637
NDRG3 Layer 4 2.7012 0.7633
SNAP91 Layer 4 2.7480 0.7628
SULT4A1 Layer 4 2.6719 0.7626
NRN1 Layer 4 2.9023 0.7624
SNX10 Layer 3 2.6250 0.7622
OAT Layer 4 2.5391 0.7614
DCLK1 Layer 4 2.6777 0.7612
KCNA2 Layer 4 3.0059 0.7611
CHGA Layer 4 2.7188 0.7599
ATP13A2 Layer 3 2.4785 0.7584
INA Layer 3 2.8555 0.7578
NSG1 Layer 4 2.8281 0.7565
GNB5 Layer 4 3.0781 0.7563
TPD52 Layer 4 2.5781 0.7557
SNCG Layer 3 2.8340 0.7557
PNKD Layer 3 2.5566 0.7548
RHEB Layer 4 2.5508 0.7540
ELMOD1 Layer 4 2.6133 0.7539
DYNLT3 Layer 3 2.5303 0.7537
KLC2 Layer 4 2.5898 0.7535
GRINA Layer 4 2.6426 0.7533
AAK1 Layer 4 2.8086 0.7531
VPS35 Layer 4 2.4941 0.7531
BMERB1 Layer 4 2.5273 0.7528
SLC12A5 Layer 4 2.9160 0.7526
SPOCK2 Layer 3 2.3926 0.7526
ATXN7L3B Layer 4 2.4883 0.7518
KIF3A Layer 4 2.5391 0.7508
CD99L2 Layer 4 2.7480 0.7506
STX1A Layer 4 2.5781 0.7506
UQCRC2 Layer 4 2.5508 0.7494
VAMP1 Layer 4 3.0391 0.7490
MYT1L Layer 4 2.7422 0.7488
ELAVL4 Layer 4 2.8711 0.7487
CAMTA1 Layer 4 2.8223 0.7478
TTC9B Layer 4 2.7188 0.7472
GABRG2 Layer 4 2.9863 0.7471
SCN1B Layer 4 3.3359 0.7465
SYNE1 Layer 3 2.5811 0.7465
SYT13 Layer 3 2.9863 0.7464
CNTNAP2 Layer 4 3.1328 0.7459
RAB3C Layer 5 2.5605 0.7456
NEUROD6 Layer 4 3.3359 0.7452

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0662
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0662_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0662/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0662/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0662/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0662/report/PD/BN0662_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0662/report/PD/BN0662_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:14:27
  • Number of Processes: 10
  • Spending Time: 0h 4m